Luskin v Tree of Life: More Troubles in the Tree of Animal Life?

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Casey Luskin exposes some of his unfamiliarity with evolutionary theory when he claims that there are “More Troubles in the Tree of Animal Life”.

And how does Luskin reach this remarkable conclusion well because of our ignorance of science.

Casey Luskin Wrote:

In late 2005, three biologists published a study in Science which concluded, “Despite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved.”

Luskin references an article in Science Daily titled Tree Of Animal Life Has Branches Rearranged, By Evolutionary Biologists to further his claims. So let’s explore Luskin’s misunderstandings and see what science does and does not know, lest one may get the impression that there is some fundamental flaw with the ‘Tree of Life’

Casey Luskin Wrote:

In 2008, the relationships among animals are still controversial. A recent news release at Science Daily highlights a new study, “Tree Of Animal Life Has Branches Rearranged.” The story reports, “The study is the most comprehensive animal phylogenomic research project to date, involving 40 million base pairs of new DNA data taken from 29 animal species.”

Luskin focuses on the ‘surprising results’ while somehow avoiding the other findings of the study

The study, which appears in Nature, settles some long-standing debates about the relationships between major groups of animals and offers up a few surprises.

Luskin seems concerned about Science rearranging the root of the tree based on new findings. I have observed that it is quite common amongst creationists to see Science’s ability and flexibility to deal with new data, as a weakness of science. To a creationist, the Truth has already been established.

Casey Luskin Wrote:

According to the article, the study yielded surprising results: “Comb jellyfish – common and extremely fragile jellies with well-developed tissues – appear to have diverged from other animals even before the lowly sponge, which has no tissue to speak of. This finding calls into question the very root of the animal tree of life, which traditionally placed sponges at the base.”

However Dunn, one of the authors of the paper in question, which was published in Nature, points out that the study has found some fascinating verifications as well as new insights into the evolution of life.

Dunn and his team:

* unambiguously confirmed certain animal relationships, including the existence of a group that includes invertebrates that shed their skin, such as arthropods and nematodes; * convincingly resolved conflicting evidence surrounding other relationships, such as the close relationship of millipedes and centipedes to spiders rather than insects; * established new animal relationships, such as the close ties between nemerteans, or ribbon worms, and brachiopods, or two-shelled invertebrates.

“What is exciting is that this new information changes our basic understanding about the natural world – information found in basic biology books and natural history posters,” Dunn said. “While the picture of the tree of life is far from complete after this study, it is clearer. And these new results show that these new genomic approaches will be able to resolve at least some problems that have been previously intractable.”

Source: Casey W. Dunn et al Broad phylogenomic sampling improves resolution of the animal tree of life, Nature (Full Text

The paper ends with the following comment

The placement of ctenophores (comb jellies) as the sister group to all other sampled metazoans is strongly supported in all our analyses. This result, which has not been postulated before, should be viewed as provisional until more data are considered from placozoans and additional sponges. If corroborated by further analyses, it would have major implications for early animal evolution, indicating either that sponges have been greatly simplified or that the complex morphology of ctenophores has arisen independently from that of other metazoans. Independent analyses of ribosomal and non-ribosomal proteins (Supplementary Information and Supplementary Fig. 10) indicate that support for this hypothesis (and for others presented for the first time here, such as Clade A and Clade B) is much greater in the combined analyses than in partitioned analyses with fewer genes. This may explain why these novel clades have not been recovered before, because support requires very broad gene sampling.

Compare this with Luskin’s description

This is the common theme among systematists trying to produce a grand “tree of life”: Similarities between different types of organisms commonly pop up in places they shouldn’t. Such unexpected similarities were found in this study, forcing one of the scientists to conclude “either that comb jellies evolved their complexity independently from other animals, [or] sponges have become greatly simplified through the course of evolution.”

Unexpected does not mean wrong, just that new data resolves some of the details. First of all, the data needs to be confirmed but furthermore, it has opened up evolutionary theory to more exciting hypotheses that will further new research.

What has Intelligent Design to offer here? Luskin does not explain, other than a strange story about Atlantis and a conclusion that “The other possibility is that there is no Atlantis to find and that people are mistaken in their various theories about how to find Atlantis.”

Atlantis has never been found, the Tree of Life, while well resolved at some aspects, needs more work to figure out the details in the evolutionary history of the millions of species involved.

For those interested in reading more about the this see for instance 29+ Evidences for Macroevolution by Douglas Theobald, Ph.D. (a little dated)

As to why morphological and genetic trees can and do conflict, see for instance Molecular versus Morphological Data in Systematic Studies

Now let me be the first one to point out that much of the Tree of Life remains unknown, although some important aspects have been successfully resolved. Does this mean that additional data is not going to add or overturn parts of the TOL? Of course not, what ID sees as a weakness of evolutionary theory and science is general is how science iterates between data, hypotheses, more data, some hypotheses rejected, more hypotheses and so on, towards an ever increasing understanding of how life evolved.

29 Comments

The DI hacks are, by and large, very clever propagandists and PR flacks.

I used to think that Casey was also one of these very clever propagandists. He seems to follow their form, but the poor devil exhibits most of the symptoms of pure good old fashioned stupidity.

An “earth scientist” and “attorney” who apparently sits around all day Googling his name and sifting thru science journals looking for honest science to mangle and misrepresent.

PvM Wrote:

For those interested in reading more about the this see for instance 29+ Evidences for Macroevolution by Douglas Theobald, Ph.D. (a little dated)

Maybe some examples need updating, but it’s overall message becomes more relevant each day, as anti-evolution activists steadfastly refuse to take Dr. Theobald up on his potential falsifiers, and instead recycle the same old long-refuted misrepresentations.

Instead of concentrating on the surprises in the new data, why not concentrate on the confirmations of previous hypotheses. How do creationists explain the branch points that are well supported by many different data sets? How do they explain the fact that we are able to reconstruct a tree of life at all?

We find strong support at all key internal arthropod nodes, and several contentious relationships of central interest are well resolved for the first time. Pycnogonids (sea spiders) group with chelicerates, rejecting placement of sea spiders as the earliest branching arthropod lineage.

Quick, someone should tell PZ:

As I mentioned above, this observation does shake up the arthropod family tree a bit. Below are two different cladograms. The right side is the current view, with the Pycnogonida and Chelicerata as sister clades, more closely related to each other than to the Mandibulata, insects and crustaceans. This view assumes chelicerae and chelifores are homologous structures. On the left side is the cladogram if they are not homologous, and the chelifore is instead homologous to the great appendage of the stem arthropods.

Oh, right, someone did already:

I reported on a study of pycnogonids, the sea spiders, that appeared to show that that might not be the case: on the basis of neural organization and innervation, that study showed that the way pycnogonid chelifores (a pair of large, fang-like structures at the front of the head) were innervated suggested that they were homologous to great appendages. I thought that was pretty darned cool; a relic of a grand Cambrian clade was swimming around in our modern oceans.

However, a new report by Jager et al. suggests that that interpretation may be flawed, and that sea spider chelifores are actually homologous to the chelicerae of spiders. […] Sea spider larvae have patterns of gene expression that line up perfectly with what we see in more ordinary spiders—chelifores and chelicerae are homologous.

So, perhaps the end of that particular puzzle. Someone should teach creationists that the only thing cooler than data is more data. (And may I add that genetics is teh hawt?)

“Sea spider larvae have patterns of gene expression that line up perfectly with what we see in more ordinary spiders—chelifores and chelicerae are homologous.”

On another thread, someone was trying to claim that our knowledge of developmental genetics did not give us any knowledge about the processes involved in evolution. Well here is another perfect example of how the understanding of basic developmental processes and changes in those processes tells us a great deal about both the pattern and process of evolution.

In this case, the pattern of gene expression helps to determine homology among anatomical structures. It also helps to show how changes in the pattern of gene expression brought about the anatomical changes that actually produced the different body plans.

As evo devo advances, creationists of all sorts will have an increasingly difficult time deyning the reality of evolution.

Nobody should be surprised by this. After all it’s Casey’s job to misunderstand evolution. In palaeontology, as in archaeology, more ancient information is less complete and therefore more subject to revision. As with other evolutionary principles, it’s Casey’s job to misunderstand.

As to why morphological and genetic trees can and do conflict, see for instance Molecular versus Morphological Data in Systematic Studies

If it gives a little more support and comfort, there are analogs to genetic and morphological trees at nearly every level of evolving systems, even in inorganic systems.

At the one of the simplest levels, the growth of crystals (e.g., ice) can take on vastly different morphological structures even though the underlying mechanisms of molecular bonding under Van der Waal forces are the same. Environmental conditions such as subtle temperature and pressure differences can make huge differences ranging from dendritic forms to flat hexagonal forms to hexagonal cylinders in the formation of ice.

The characteristics of a given solid can be significantly changed by the inclusion of defects in its crystalline structure.

Small amounts of doping in semiconductors and semimetals make huge differences in their macroscopic characteristics such as electrical and thermal conductivities, color, etc..

Even at these simplest of levels, macroscopic characteristics and emergent properties are extremely sensitive to infinitesimally small changes in the underlying processes leading to the overall development of the solid or liquid or other system.

If one were to classify even these simplest of systems according to some of their emergent characteristics, such a classification scheme would produce groups that are quite different from those in a classification scheme that relied on their underlying atomic or molecular structure.

If the ID/Creationists want to make a big deal of classification schemes to confuse rubes and the public, simple systems such as these can be used to help remove confusion.

On the other hand, perhaps it would be more fun to point out all the classification schemes that can be obtained from looking at their fragmented sectarian views. The “Big Tent” is one classification scheme that makes them all appear of the same lineage. Look more closely (more “microscopically”), change the classification scheme a little, and we see something quite different.

Luskin is such a schmuck.

Torbjörn Larsson, OM Wrote:

So, perhaps the end of that particular puzzle. Someone should teach creationists that the only thing cooler than data is more data. (And may I add that genetics is teh hawt?)

They (the scammers if not the scammed) know that already. The more data, the more to cherry pick to bolster their incredulity arguments.

Oh, damn. And the more the data, the more the gaps as well.

But I come from the glass half full part of the world. Can I have a lemon slice with that instead, please, I’m no big fan of cherries?

Atlantis has been found. There is a lot of convincing evidence that the myth of Atlantis actually refers to the Aegean archipelago of Santorini.

Luskin is making no mistake in his writings. As pointed out by waldteufel, et. al., “The DI hacks are, by and large, very clever propagandists and PR flacks,”

Luskin and his creationist colleagues at the DI and elsewhere are very successful in what they do. That’s the whole point. He’s selling his storys to other creationists who are too stupid to check any facts or writings, but take people like Luskin at their word, that they are telling the truth. Would a religious person ever lie? Not to them, because that’s what they want to believe, so no matter what any scientist says, the creationist can mangle it all he wants & get away with it. They write for the popular press, they take their case to the public. It’s all a PR stunt that they’ve honed to a fine art and can be relatively successful at it. Teach the controversy, freedom of speech, buzz words that work for them.

It’s a sad state and most unfortunate, but we have to continue to deal with them.

Thanks Reed, makes the Luskin story even more ironic.

If one were to classify even these simplest of systems according to some of their emergent characteristics, such a classification scheme would produce groups that are quite different from those in a classification scheme that relied on their underlying atomic or molecular structure.

If only the ID/creationism ‘theorists’ could wrap their mind about just this simple (as far as my mind sees) concept.

Or am I wrong in seeing much of creationist opinion on scientific matters like just a vulgar reductionism ad absurdum?

The key point is in the title of the paper; “improves”.

Atlantis has been found. There is a lot of convincing evidence that the myth of Atlantis actually refers to the Aegean archipelago of Santorini.

It isn’t quite as simple as that. For example Plato describes Atlantis as “larger than Libya and Asia put together”. Even allowing for ‘Asia’ just being Anatolia, this clearly does not apply to Santorini. But it is reasonable to consider the myth to be partly inspired by the events at Santorini.

Les Lane Wrote:

After all it’s Casey’s job to misunderstand evolution.

The more appropriate word is “misrepresent.” These people can’t possibly “misunderstand” evolution as thoroughly as they appear to at first glance, if only because they always know what to take out of context, and how to spin it to impress the rubes.

Before I get the usual reaction from those who prefer to portray them as honest-but-clueless instead of shrewd scam artists, I’m in no way implying that they understand evolution as well as the average PhD biologist. Just more than they let on.

Frank J:

Les Lane Wrote:

After all it’s Casey’s job to misunderstand evolution.

The more appropriate word is “misrepresent.” These people can’t possibly “misunderstand” evolution as thoroughly as they appear to at first glance, if only because they always know what to take out of context, and how to spin it to impress the rubes.

Before I get the usual reaction from those who prefer to portray them as honest-but-clueless instead of shrewd scam artists, I’m in no way implying that they understand evolution as well as the average PhD biologist. Just more than they let on.

It’s my opinion, especially after engaging in that thoroughly unpleasant thread with Salvador Cordova, that the people of the Discovery Institute both misunderstand AND misrepresent Evolutionary Biology. This way, in their guise of (false) authority, they not only give their flock an extra helping of stupidity, but also immunize them against people who actually know about Biology, Evolutionary or otherwise.

Stanton,

It’s not a question that they misunderstand evolution, but to what extent. And I think we all need to admit that they are probably not as clueless as they come across.

From my recent discussions with Salvador, he appears to be quite different than the rest of the DI gang. With the usual caveat that we cannot really know another’s private thoughts, my impression is that he exhibits a degree of honesty that is almost completely lacking in the others. His candid admissions (i.e. YEC is 85% likely yet still “fringe”) seem to show the effects of Morton’s Demon filtering the information. In contrast, the “don’t ask, don’t tell” approach, coupled with the occasional concession to mainstream science and calculated bait-and-switch of definitions and concepts, all suggest some private knowledge that mainstream science may be right. Knowledge that they would not dare admit to their target audience.

On the other hand, Frank, he did subtly admit that he finds Young Earth Creationism more convincing, at least that he finds the idea that terrestrial animals are descended from the pairs Noah brought into the Ark.

Stanton,

IIRC, Cordova even said that the Bible should be used as evidence, while Behe said that doing so is “silly.” From my limited personal experience, those more like Cordova eventually become Omphalos creationists (admitting that the evidence does not support YEC but that the Bible overrules the evidence), and those more like Behe grudgingly concede evolution “or something like it.” OTOH, they did not have a prior commitment to misleading the public.

I’ve also often wondered about the issue of clueless idiot versus confidence trickster.

I venture to suggest that neither is the case. With the same caveat that Frank J makes, I propose that the frame of mind of the DI-ers is more that of people entering a debating contest with prize money. Their interest is in winning the contest, and they consider the actual accuracy of the positions taken to be irrelevant. They aren’t deliberately and consciously twisting the truth: they just aren’t interested in the truth. Only debating points matter.

Winning in this case presumably entails a sufficient flow of cash to the DI to give them a continuing income.

Of course, because this is about the real world, not a mere debating contest, the end result is that they are dishonest. But I don’t think that’s actually their conscious intention.

At least Behe retains enough scientific baggage to be somewhat interested in the truth, hence his admission of the common descent of humans and chimpanzees. (Have any of the other DI-ers ever commented on that, by the way?)

When the story first appeared on Science Daily, the illustration was of hydrozoan medusae. Now the illustration is indeed of a ctenophore. Surely this is an example of regressive evolution guided by ID.

Stephen Wrote:

(Have any of the other DI-ers ever commented on that, by the way?)

Yes, but none have directly challenged him on it (as any real scientist would be eager to do), though several attempted damage control, which is expected given their mostly YEC audience.

Most DI fellows seem “unconvinced” of common descent (most also admit mainstream chronology, but that’s another story). But note that they never say that they are convinced of the alternative, which is by definition, independent abiogenesis of lineages.

IDers invariably bait-and-switch between CD as science defines it (Precambrian horizontal transfer and all) and a “universal” CD caricature (everything descended from a single cell). The closer they get to apes and humans the more fuzzy they get, because they know that it’s one thing to suggest that archaea and eubacteria may have been products of independent abiogenesis events, but for eukaryotes as similar as humans and other apes to have originated independently is an extraordinary claim that demands extraordinary evidence that is simply not there.

Several months ago I read second hand that Dembski rejected common ancestry of humans and other apes. When I checked his own words all he said was that he doubted that they evolved from common ancestors (IOW, he did not rule out in vivo “saltation”).

Why do West and Luskin blather on the “Cambrian Explosion” and on “phyla” ? The concept of phylum only makes sense in a context of common descent. If any and all creatures are created anew, why should they belong to one phylum ? Or does it means that the Creator (Designer) had a very narrow range of possible body plans ? Why ??

Still a bit OT:

Stephen said:

Atlantis has been found. There is a lot of convincing evidence that the myth of Atlantis actually refers to the Aegean archipelago of Santorini.

It isn’t quite as simple as that. For example Plato describes Atlantis as “larger than Libya and Asia put together”. Even allowing for ‘Asia’ just being Anatolia, this clearly does not apply to Santorini. But it is reasonable to consider the myth to be partly inspired by the events at Santorini.

It would be better to say that it is probable that Plato’s inspiration for Atlantis is the eruption of Santorini, which may have been instrumental in the demise of the Minoan Civilization, based on Crete, not Santorini. Plato (hmmm, possibly like some of the authors of the Bible?) was probably using historical events to craft a morality tale about the dangers of pride. The details of Atlantis, such as size, should not be considered, even to the author, as having been true.

Please return to the discussion of the dishonesty, misunderstandings, and incompetence of the DI and its minions. I’m enjoying it.

Stephen:

It isn’t quite as simple as that. For example Plato describes Atlantis as “larger than Libya and Asia put together”. Even allowing for ‘Asia’ just being Anatolia, this clearly does not apply to Santorini. But it is reasonable to consider the myth to be partly inspired by the events at Santorini.

The explanation that I’ve heard is that the myth was translated into Greek from Egyptian, and an error increased the size of the land mass by a factor of 10.

David Stanton:

As evo devo advances, creationists of all sorts will have an increasingly difficult time deyning the reality of evolution.

I think you are severely underestimating the denial skillz of the creationists.

Chad:

David Stanton:

As evo devo advances, creationists of all sorts will have an increasingly difficult time deyning the reality of evolution.

I think you are severely underestimating the denial skillz of the creationists.

Yes, these nuts will walk a hundred miles barefoot for a lie, rather than look at the facts right in front of them.

Updated genesis of “tree of life”

Genes Are Primal And Genomes Are Evolved Organisms

A. In view of the information we now have about life and its evolution:

Earth Life: 1. a format of temporarily constrained energy, retained in temporary constrained genetic energy packages in forms of genes, genomes and organisms 2. a real virtual affair that pops in and out of existence in its matrix, which is the energy constrained in Earth’s biosphere.

Earth organism: a temporary self-replicable constrained-energy genetic system that supports and maintains Earth’s biosphere by maintenance of genes.

Gene: a primal Earth’s organism.

Genome: a multigenes organism consisting of a cooperative commune of its member genes.

Cellular organisms: mono- or multi-celled earth organisms.

B. Update of life sciences conceptions is now feasible and urgently desirable:

- First were independent individual genes, Earth’s primal organisms.

- Genes aggregated cooperatively into genomes, multigenes organisms, with genomes’ organs.

- Simultaneously or consequently genomes evolved protective and functional membranes, organs.

- Then followed cellular organisms, with a variety of outer-cell membranes shapes and functionalities.

This conception is a scientific, NOT TECHNOLOGICAL, life-science innovation.

It is tomorrow’s comprehension of life and its evolution.

IT EVOKES INTRIGUING DARWINIAN IMPLICATIONS.

IT IS FRAUGHT WITH INTRIGUING TECHNOLOGICAL DEVELOPMENTS POTENTIALS.

Suggesting,

Dov Henis

http://blog.360.yahoo.com/blog-P81p[…]BbHgtjQjxG_Q–?cq=1

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This page contains a single entry by PvM published on March 22, 2008 7:17 PM.

Phyloinformatics Summer of Code 2008 was the previous entry in this blog.

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